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https://github.com/bioconductor-source/readat

https://github.com/bioconductor-source/readat

Science Score: 26.0%

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Repository

Basic Info
  • Host: GitHub
  • Owner: bioconductor-source
  • Language: R
  • Default Branch: devel
  • Size: 1.25 MB
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Created almost 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog

README.md

Project Status: Active - The project has reached a stable, usable state and is being actively developed. Build Status Build status

readat

Tools for importing and working with SomaLogic ADAT files.

Read the paper in BMC Bioinformatics: readat: An R package for reading and working with SomaLogic ADAT files

Installation

To install the package, you first need the devtools package.

{r} install.packages("devtools")

Then you can install the readat package using

{r} devtools::install_bitbucket("graumannlabtools/readat")

Functionality

readAdat let's you import data from the SomaLogic ADAT file format. The result is stored in an object of class WideSomaData. This is a data.table with one sample per row, and includes both the intensities and sample metadata. The object also has an attribute named sequenceData that contains a data.table of sequence metadata. There are also attributes for experiment metadata and a checksum.

getSequenceData, getMetadata, and getChecksum provide shortcuts to access these attributes.

There is a melt method for WideSomaData that converts the object to LongSomaData format, which is a data.table with one intensity per row.

soma2eset converts an object of class WideSomaData to a Biobase::ExpressionSet.

You can retrieve additional annotations by SomaLogic Sequence ID uisng getEnsemblIds, getUniProtKeywords, getChromosomalPositions, getPfam, getKeggDefinitions, getKeggModules, getKeggPathways, getGoMolecularFunctions, getGoBiologicalProcesses, getGoCellularComponents.

getSequencesWithLargestBetweenGroupVariation find the sequences with the largest amount of variation between specified sample groups.

Owner

  • Name: (WIP DEV) Bioconductor Packages
  • Login: bioconductor-source
  • Kind: organization
  • Email: maintainer@bioconductor.org

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Dependencies

DESCRIPTION cran
  • R >= 3.4.0 depends
  • Biobase >= 2.34.0 imports
  • SummarizedExperiment >= 1.4.0 imports
  • assertive.base >= 0.0 imports
  • assertive.files >= 0.0 imports
  • assertive.numbers >= 0.0 imports
  • assertive.properties >= 0.0 imports
  • assertive.sets >= 0.0 imports
  • assertive.types >= 0.0 imports
  • data.table >= 1.10.4 imports
  • dplyr >= 0.5.0 imports
  • magrittr >= 1.5 imports
  • openxlsx >= 4.0.17 imports
  • pathological >= 0.1 imports
  • reshape2 >= 1.4.2 imports
  • stats * imports
  • stringi >= 1.1.5 imports
  • testthat >= 1.0.2 imports
  • tidyr >= 0.6.2 imports
  • utils * imports
  • MSnbase * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • withr * suggests